Add taxonomy to Gene model

backend/metagenedb/apps/catalog/admin/gene.py

@@ -6,9 +6,17 @@ from metagenedb.apps.catalog.models import Gene
 @admin.register(Gene)
 class GeneAdmin(admin.ModelAdmin):
 
-    list_display = ('gene_id', 'gene_length', 'get_functions')
+    list_display = ('gene_id', 'gene_length', 'get_functions', 'get_taxonomy')
     search_fields = ('gene_id',)
 
     def get_functions(self, obj):
-        return ",".join([str(f) for f in obj.functions.all()])
+        if obj.functions.all():
+            return ",".join([str(f) for f in obj.functions.all()])
+        return '-'
     get_functions.short_description = 'Functions'
+
+    def get_taxonomy(self, obj):
+        if obj.taxonomy:
+            return f"{obj.taxonomy} ({obj.taxonomy.rank})"
+        return '-'
+    get_taxonomy.short_description = 'Taxonomy'

backend/metagenedb/apps/catalog/migrations/0006_gene_taxonomy.py

+# Generated by Django 2.2.1 on 2019-08-05 13:45
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0005_gene_ordering'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='gene',
+            name='taxonomy',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='genes', to='catalog.Taxonomy'),
+        ),
+    ]

backend/metagenedb/apps/catalog/models/gene.py

@@ -7,6 +7,11 @@ class Gene(models.Model):
     gene_id = models.CharField(max_length=100, unique=True, db_index=True)
     gene_length = models.IntegerField()
     functions = models.ManyToManyField(Function)
+    taxonomy = models.ForeignKey(
+        'Taxonomy', related_name='genes',
+        on_delete=models.SET_NULL,
+        null=True, blank=True
+    )
 
     def __str__(self):
         return self.gene_id

backend/metagenedb/apps/catalog/serializers/gene.py

 from rest_framework import serializers
-from metagenedb.apps.catalog.models import Gene
+from metagenedb.apps.catalog.models import Gene, Taxonomy
 from metagenedb.apps.catalog.serializers import FunctionSerializer
 
 
 class GeneSerializer(serializers.ModelSerializer):
     functions = FunctionSerializer(many=True, read_only=True)
+    taxonomy = serializers.SlugRelatedField(
+        queryset=Taxonomy.objects.all(),
+        slug_field='tax_id',
+        required=False,
+    )
 
     class Meta:
         model = Gene
-        fields = ('gene_id', 'gene_length', 'functions')
+        fields = ('gene_id', 'gene_length', 'functions', 'taxonomy')

backend/scripts/populate_db/import_igc_data.py

@@ -14,13 +14,15 @@ from metagenedb.common.utils.parsers import IGCLineParser
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "metagenedb.settings")
 django.setup()
 
-from metagenedb.apps.catalog.models import Gene, Function  # noqa
+from metagenedb.apps.catalog.models import Gene, Function, Taxonomy  # noqa
 from metagenedb.apps.catalog.serializers import GeneSerializer  # noqa
 
 logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
-SELECTED_KEYS = ['gene_id', 'gene_length', 'kegg_ko']
+PHYLUM_COL = 'taxo_phylum'
+GENUS_COL = 'taxo_genus'
+SELECTED_KEYS = ['gene_id', 'gene_length', 'kegg_ko', PHYLUM_COL, GENUS_COL]
 
 
 def parse_gene(raw_line, selected_keys=SELECTED_KEYS):
@@ -33,6 +35,30 @@ def parse_gene(raw_line, selected_keys=SELECTED_KEYS):
     return selected_dict
 
 
+def select_taxonomy(gene_dict, unknown_val='unknown'):
+    """
+    Select the taxonomy to be assigned for the gene.
+    genus has priority on phylum. If both unknow, remove the taxonomy key
+    """
+    phylum = gene_dict.pop(PHYLUM_COL)
+    genus = gene_dict.pop(GENUS_COL)
+    if genus != unknown_val:
+        queryset = Taxonomy.objects.filter(name=genus, rank="genus")
+        if queryset.count() > 1:
+            _LOGGER.warning(f"More than 1 result found for genus {genus}. First result is kept.")
+        gene_dict.update(
+            {'taxonomy': queryset[0].tax_id}
+        )
+    elif phylum != unknown_val:
+        queryset = Taxonomy.objects.filter(name=phylum, rank="phylum")
+        if queryset.count() > 1:
+            _LOGGER.warning(f"More than 1 result found for phylum {phylum}. First result is kept.")
+        gene_dict.update(
+            {'taxonomy': queryset[0].tax_id}
+        )
+    return gene_dict
+
+
 def upsert_gene(gene_dict):
     try:
         gene_obj = Gene.objects.get(gene_id=gene_dict.get('gene_id'))
@@ -46,8 +72,9 @@ def upsert_gene(gene_dict):
 def insert_gene_list(chunk_genes):
     for gene_line in chunk_genes:
         gene_dict = parse_gene(gene_line)
+        gene_dict_with_taxo = select_taxonomy(gene_dict)
         try:
-            upsert_gene(gene_dict)
+            upsert_gene(gene_dict_with_taxo)
         except ValidationError as e:
             _LOGGER.warning(f"{e.__dict__} for gene_id: {gene_dict.get('gene_id')}. Insertion skipped.")
 

backend/scripts/populate_db/test_import_igc_data.py

@@ -4,7 +4,7 @@ from rest_framework.exceptions import ValidationError
 from rest_framework.test import APITestCase
 
 from metagenedb.apps.catalog.models import Gene
-from scripts.populate_db.import_igc_data import parse_gene, upsert_gene
+from scripts.populate_db.import_igc_data import parse_gene, upsert_gene, select_taxonomy
 
 
 class TestParseGene(TestCase):
@@ -35,7 +35,9 @@ class TestParseGene(TestCase):
         expected_dict = {
             'gene_id': 'gene_name',
             'gene_length': 'gene_length',
-            'kegg_ko': 'kegg'
+            'kegg_ko': 'kegg',
+            'taxo_phylum': 'taxo_phylum',
+            'taxo_genus': 'taxo_genus',
         }
         tested_dict = parse_gene(self.raw_line)
         self.assertDictEqual(tested_dict, expected_dict)
@@ -96,3 +98,29 @@ class TestUpsertGene(APITestCase):
         self.assertEqual(Gene.objects.get(gene_id="test_gene01").gene_length, 3556)
         upsert_gene(updated_gene)
         self.assertEqual(Gene.objects.get(gene_id="test_gene01").gene_length, 356)
+
+
+class TestSelectTaxonomy(TestCase):
+
+    def test_genus_only(self):
+        pass  # @TODO with #31
+
+    def test_phylum_only(self):
+        pass  # @TODO with #31
+
+    def test_genus_phylum(self):
+        pass  # @TODO with #31
+
+    def test_both_unknown(self):
+        gene_dict = {
+            'gene_id': 'gene',
+            'gene_length': 135,
+            'taxo_phylum': 'unknown',
+            'taxo_genus': 'unknown'
+        }
+        expected_dict = {
+            'gene_id': 'gene',
+            'gene_length': 135
+        }
+        tested_dict = select_taxonomy(gene_dict)
+        self.assertDictEqual(tested_dict, expected_dict)